## [1] "Wed Jan 31 13:11:39 2024"
## [1] "LOINC codes for chemical tests: loinc_data/loinc_chem_names.tsv"
## [1] "LOINC codes: 10606"
NER = named entity recognition, a form of text-mining.
## [1] "NextMove NER for LOINC-component: loinc_data/loinc_chem_names_2_NM_CFDictGeneAndProtein_leadmine.tsv"
## [1] "LOINC codes mapped via component text to NER proteins: 1878"
## [1] "LOINC codes resolved to standard IDs: 990 / 1878"
## [1] "LOINC codes resolved to HGNC IDs: 809 / 1878"
## [1] "LOINC codes resolved to UniProt IDs: 50 / 1878"
## [1] "LOINC codes resolved to Entrez (gene?) IDs: 132 / 1878"
Cerner Real World Data 2023 counts of distinct encounter_ids and patient_ids for LOINC codes of class “CHEM”. Each count is for a specific lab test, and year. Some different labs have same LOINC codes, i.e. some Cerner-coded lab tests merge to the same LOINC code. Also, the counts cannot be added, since there may be common patients and encounters.
## [1] "LOINC codes in RWD encounters: 3593"
## [1] "Number of labs tests which merge to a common LOINC, in representative year 2021: 9 / 2981"
Encounter ID counts can be added for multiple years, but not patient ID counts, since there can be common ID. When added over multiple labs, encounter ID counts should be interpreted as lab counts, since a single encounter can involve multiple labs.
## [1] "Total LOINCs: 3593; total lab-encounters: 8e+10"
## [1] "LOINC codes for proteins in RWD encounters: 868"
## [1] "LOINC protein names in RWD encounters: 421"
For now, remove data without resolved protein IDs. And the few Ensembl IDs, pending clarification on ENSG vs ENSP.
| loinc_code | geneOrProteinId | mnemonics | lab_count |
|---|---|---|---|
| 1751-7 | HGNC:399 | Albumin [Mass/volume] in Serum or Plasma | 99530276 |
| 1742-6 | HGNC:4552 | Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma | 99448917 |
| 1759-0 | HGNC:399 | Albumin/Globulin [Mass Ratio] in Serum or Plasma | 47030076 |
| 1968-7 | HGNC:399 | Bilirubin.direct [Mass/volume] in Serum or Plasma | 39076770 |
| 3040-3 | HGNC:6619 | Lipase [Enzymatic activity/volume] in Serum or Plasma | 36872904 |
| 1743-4 | HGNC:4552 | Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma by With P-5’-P | 15184942 |
| 61152-5 | HGNC:399 | Albumin [Mass/volume] in Serum or Plasma by Bromocresol purple (BCP) dye binding method | 11031598 |
| 1744-2 | HGNC:4552 | Alanine aminotransferase [Enzymatic activity/volume] in Serum or Plasma by No addition of P-5’-P | 10648619 |
| 2857-1 | UNIPROT:P07288 | Prostate specific Ag [Mass/volume] in Serum or Plasma | 9823612 |
| 61151-7 | HGNC:399 | Albumin [Mass/volume] in Serum or Plasma by Bromocresol green (BCG) dye binding method | 9233502 |
| 2276-4 | UNIPROT:Q26061 | Ferritin [Mass/volume] in Serum or Plasma | 8445047 |
| 14957-5 | HGNC:399 | Microalbumin [Mass/volume] in Urine | 6172810 |
| 2502-3 | HGNC:11740 | Iron saturation [Mass Fraction] in Serum or Plasma | 5600674 |
| 14959-1 | HGNC:399 | Microalbumin/Creatinine [Mass Ratio] in Urine | 4458248 |
| 2731-8 | HGNC:9606 | Parathyrin.intact [Mass/volume] in Serum or Plasma | 3020605 |
| 14338-8 | HGNC:399 | Prealbumin [Mass/volume] in Serum or Plasma | 2754876 |
| 2324-2 | UNIPROT:P63186 | Gamma glutamyl transferase [Enzymatic activity/volume] in Serum or Plasma | 2406028 |
| 3034-6 | HGNC:11740 | Transferrin [Mass/volume] in Serum or Plasma | 2160471 |
| 1754-1 | HGNC:399 | Albumin [Mass/volume] in Urine | 2077739 |
| 1747-5 | HGNC:399 | Albumin [Mass/volume] in Body fluid | 1764137 |
| 2874-6 | UNIPROT:Q65479 | Gamma globulin [Mass/volume] in Serum or Plasma by Electrophoresis | 1405639 |
| 9318-7 | HGNC:399 | Albumin/Creatinine [Mass Ratio] in Urine | 1365878 |
| 1916-6 | HGNC:4552 | Aspartate aminotransferase/Alanine aminotransferase [Enzymatic activity ratio] in Serum or Plasma | 1286362 |
| 2862-1 | HGNC:399 | Albumin [Mass/volume] in Serum or Plasma by Electrophoresis | 1283018 |
| 44429-9 | HGNC:399 | Albumin/Globulin [Mass Ratio] in Serum or Plasma by Electrophoresis | 1280969 |
| 10501-5 | UNIPROT:P01231 | Lutropin [Units/volume] in Serum or Plasma | 1076989 |
| 2842-3 | HGNC:9445 | Prolactin [Mass/volume] in Serum or Plasma | 1059015 |
| 46099-8 | HGNC:399 | Calcium [Mass/volume] corrected for albumin in Serum or Plasma | 988146 |
| 2639-3 | HGNC:6915 | Myoglobin [Mass/volume] in Serum or Plasma | 987685 |
| 1834-1 | HGNC:317 | Alpha-1-Fetoprotein [Mass/volume] in Serum or Plasma | 774174 |
| 20448-7 | HGNC:6081 | Insulin [Units/volume] in Serum or Plasma | 703189 |
| 1825-9 | UNIPROT:P22922 | Alpha 1 antitrypsin [Mass/volume] in Serum or Plasma | 699936 |
| 13967-5 | HGNC:10839 | Sex hormone binding globulin [Moles/volume] in Serum or Plasma | 624428 |
| 76625-3 | HGNC:4552 | Alanine aminotransferase [Enzymatic activity/volume] in Blood | 619940 |
| 50949-7 | HGNC:399 | Albumin [Presence] in Urine by Test strip | 615220 |
| 10886-0 | UNIPROT:P07288 | Prostate Specific Ag Free [Mass/volume] in Serum or Plasma | 509922 |
| 6875-9 | UNIPROT:P15941 | Cancer Ag 15-3 [Units/volume] in Serum or Plasma | 493760 |
| 20567-4 | UNIPROT:Q26061 | Ferritin [Mass/volume] in Serum or Plasma by Immunoassay | 478926 |
| 53962-7 | HGNC:317 | Alpha-1-fetoprotein.tumor marker [Mass/volume] in Serum or Plasma | 459542 |
| 46761-3 | HGNC:1122 | Biotinidase deficiency newborn screen interpretation | 452287 |
| 12841-3 | UNIPROT:P07288 | Prostate Specific Ag Free/Prostate specific Ag.total in Serum or Plasma | 429179 |
| 2742-5 | HGNC:2707 | Angiotensin converting enzyme [Enzymatic activity/volume] in Serum or Plasma | 420194 |
| 33358-3 | UNIPROT:P54296 | Protein.monoclonal [Mass/volume] in Serum or Plasma by Electrophoresis | 420043 |
| 15061-5 | HGNC:3415 | Erythropoietin (EPO) [Units/volume] in Serum or Plasma | 410958 |
| 17842-6 | UNIPROT:Q02496 | Cancer Ag 27-29 [Units/volume] in Serum or Plasma | 393225 |
| 32769-2 | UNIPROT:P22922 | Alpha 1 antitrypsin phenotype [Interpretation] in Serum or Plasma; Alpha 1 antitrypsin phenotyping [Interpretation] in Serum or Plasma | 382692 |
| 32769-2 | UNIPROT:P22922 | Alpha 1 antitrypsin phenotyping [Interpretation] in Serum or Plasma; Alpha 1 antitrypsin phenotype [Interpretation] in Serum or Plasma | 382692 |
| 32769-2 | UNIPROT:P22922 | Alpha 1 antitrypsin phenotype [Interpretation] in Serum or Plasma | 382692 |
| 2484-4 | HGNC:5464 | Insulin-like growth factor-I [Mass/volume] in Serum or Plasma | 345762 |
| 3013-0 | HGNC:11764 | Thyroglobulin [Mass/volume] in Serum or Plasma | 317568 |